Just a tip: I love the Exclude Pages plugin, but I noticed it if the "include in navigation" box wasn't explicitly declared as checked, pages would remain hidden. This is a problem when another plugin (in my case nextgen gallery) created pages transparently- I couldn't get those pages to show up by default.
The fix: Switch!
I just changed the default to be SHOW this page, and the checkbox explicitly EXCLUDES pages from navigation.
I hope I got this right, you can see and copy changes here: